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Estimated time of infection vs. confirmed infections

Following the ideas from Tomas Pueyo's Medium post "Coronavirus: Why You Must Act Now" [1], we assume the average time from infection to death at 23 days [2]. The data is pulled from the COVID-19 Data Repository by Johns Hopkins CSSE [3] every hour. Countries with a minimnum of 1000 confirmed cases and 40 confirmed deaths are included in this analysis.

The time from infection to death is equal to the incubation period plus the time from symptoms to death. This is used to estimate the time of the infections that lead to the observed deaths. We take the last fatality rate per country (total_cases/total_deaths) to estimate the number of infections that are responsible for the observed deaths.

In the figures below, you can observe successive waves of infections (dashed), detections (black) and deaths (red) for each country. The upper panel shows the absolute number of events. The dashed lines show the estimated number of infections. The lower panel shows the normalized number of events. Here the temporal delay between the waves and the relative change between each other can be observed.

[1] https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca

[2] https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus

[3] https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series

US
Brazil
India
Mexico
Peru
Russia
United Kingdom
Indonesia
Italy
Colombia
France
Argentina
Iran
Germany
Spain
South Africa
Poland
Ukraine
Turkey
Chile
Romania
Philippines
Ecuador
Czechia
Hungary
Canada
Bangladesh
Pakistan
Belgium
Tunisia
Iraq
Bulgaria
Bolivia
Netherlands
Portugal
Egypt
Malaysia
Japan
Paraguay
Burma
Sweden
Greece
Kazakhstan
Slovakia
Morocco
Guatemala
Thailand
Switzerland
Austria
Vietnam
Nepal
Jordan
Bosnia and Herzegovina
Honduras
Sri Lanka
Saudi Arabia
Croatia
Lebanon
Serbia
Georgia
Afghanistan
Panama
Israel
Moldova
Uruguay
North Macedonia
Azerbaijan
Costa Rica
Algeria
Cuba
Ireland
Armenia
Kenya
Ethiopia
China
Lithuania
Slovenia
Zimbabwe
Libya
Oman
Dominican Republic
Venezuela
Belarus
West Bank and Gaza
Zambia
Namibia
Uganda
El Salvador
Sudan
Denmark
Latvia
Kyrgyzstan
Albania
Kosovo
Nigeria
Kuwait
South Korea
Botswana
Malawi
United Arab Emirates
Syria
Cambodia
Mozambique
Senegal
Montenegro
Jamaica
Bahrain
Cameroon
Estonia
Trinidad and Tobago
Angola
Eswatini
Rwanda
Uzbekistan
Congo (Kinshasa)
Finland
Ghana
Australia
Somalia
Madagascar
Mongolia
Taiwan*
Luxembourg
Norway
Suriname
Mauritania
Guyana
Qatar
Haiti
Mali
Cyprus
Fiji
Malta
Cote d'Ivoire
Lesotho
Belize
Bahamas
Guinea
Cabo Verde
Maldives
Hong Kong
Nicaragua
Papua New Guinea
Congo (Brazzaville)
Togo
Burkina Faso
Gabon
Djibouti
Andorra
Benin
Tajikistan
South Sudan
Seychelles

Ahead of the curve

Some countries start testing the population earlier in the outbreak than others. The time delay between the wave of deaths and the wave of confirmed cases is indicative for how early a country is detecting new cases ahead of the increase of deaths. Earlier detection means a better chances for successful isolation of an infected person and treatment of the desease.

We measure the distance of the maximum of cumulative deaths and new deaths to the number of infections to estimate the progression of the infection across countries.

If, in the early phase of the infection wave, the number of deaths rises faster than the number of confirmed cases, the distance drops, indicating that

A comparison of countries with respect to their mean time for reponse is presented below.

To determine the above values, we plot the number of confirmed cases (solid black lines) and the number of deaths (dashed black lines). From this, we measure the distance of the day of maximum deaths (dashed red lines) to the day of confirmed cases at this y-value.

The distance is indicative for how fast the humber of confirmed cases increases comapred to the increase of the number of deaths.

US
Brazil
India
Mexico
Peru
Russia
United Kingdom
Indonesia
Italy
Colombia
France
Argentina
Iran
Germany
Spain
South Africa
Poland
Ukraine
Turkey
Chile
Romania
Philippines
Ecuador
Czechia
Hungary
Canada
Bangladesh
Pakistan
Belgium
Tunisia
Iraq
Bulgaria
Bolivia
Netherlands
Portugal
Egypt
Malaysia
Japan
Paraguay
Burma
Sweden
Greece
Kazakhstan
Slovakia
Morocco
Guatemala
Thailand
Switzerland
Austria
Vietnam
Nepal
Jordan
Bosnia and Herzegovina
Honduras
Sri Lanka
Saudi Arabia
Croatia
Lebanon
Serbia
Georgia
Afghanistan
Panama
Israel
Moldova
Uruguay
North Macedonia
Azerbaijan
Costa Rica
Algeria
Cuba
Ireland
Armenia
Kenya
Ethiopia
China
Lithuania
Slovenia
Zimbabwe
Libya
Oman
Dominican Republic
Venezuela
Belarus
West Bank and Gaza
Zambia
Namibia
Uganda
El Salvador
Sudan
Denmark
Latvia
Kyrgyzstan
Albania
Kosovo
Nigeria
Kuwait
South Korea
Botswana
Malawi
United Arab Emirates
Syria
Cambodia
Mozambique
Senegal
Montenegro
Jamaica
Bahrain
Cameroon
Estonia
Trinidad and Tobago
Angola
Eswatini
Rwanda
Uzbekistan
Congo (Kinshasa)
Finland
Ghana
Australia
Somalia
Madagascar
Mongolia
Taiwan*
Luxembourg
Norway
Suriname
Mauritania
Guyana
Qatar
Haiti
Mali
Cyprus
Fiji
Malta
Cote d'Ivoire
Lesotho
Belize
Bahamas
Guinea
Cabo Verde
Maldives
Hong Kong
Nicaragua
Papua New Guinea
Congo (Brazzaville)
Togo
Burkina Faso
Gabon
Djibouti
Andorra
Benin
Tajikistan
South Sudan
Seychelles